Although Stonewall was set up to be a professional lobbying organisation rather than a membership organisation, it has diversified into areas such as policy development for the rights of lesbian, gay and bisexual people since Labour came into power.

However, in the last four years it has seen conspicuous successes in parliamentary lobbying. Under its previous director Angela Mason (1992 to 2002) who was awarded an OBE "for services to homosexual rights", it saw amendments to the 2002 Adoption and Children Bill which treated lesbian and gay couples in the same way as heterosexuals. Under its current Chief Executive Ben Summerskill, it was closely involved in successful parliamentary campaigns to:

introduce the 2007 Sexual Orientation Regulations, protections against discrimination on grounds of sexual orientation in the provision of goods and services secured through the Equality Act 2006.

Stonewall also works with 300 major employers across Britain providing advice and support to lesbian and gay staff. These include IBM, Credit Suisse, the Inland Revenue and the Royal Navy. An "Education for All" campaign was launched in 2005, in cooperation with 70 other organsiations, to start tackling homophobic bullying in British schools which had gone unchallenged while Section 28 was in place.

Grass-roots activists such as Peter Tatchell have accused Stonewall of endorsing discrimination by holding regular champagne receptions for celebrities and politicians supported by big businesses such as HSBC, despite that company being sued by Peter Lewis in 2005 for unfair dismissal on grounds of sexual orientation. Lewis did not win his case. Act-UP AIDS activists have also criticised Stonewall on ethical grounds for endorsing HIV drug manufacturers, including Glaxo SmithKline through its Diversity Champions initiative. The criticism of Stonewall's champagne fundraising receptions by Peter Tatchell and others was undermined when the Peter Tatchell Human Rights Fund started holding high-price ticket events (£150/$300) to raise funds itself in 2007.

Former Stonewall campaigner Chris Morris left the organisation in 1999 after becoming frustrated with the way he claimed the organisation was changing. In a column for the New Statesman magazine, offering his "explanation for the gay lobby's lack of political progress". he wrote:

"In return for their generosity, major donors are often rewarded with a place on Stonewall's board of directors and, because the organisation has supporters rather than members, these key positions are the only official way to influence Stonewall policy. A quick glance through the organisation's literature will show that yesterday's sponsors are today's decision-makers; and most key players have ongoing financial interests in lucrative gay businesses. [..] By giving financial donors the only voice in setting the agenda, gay right organisations have left themselves open to a serious charge of having a conflict of interests. Can it really just be coincidence that most groups are fighting exclusively for legal reforms and ignoring calls to tackle social prejudice, while accepting money from a business community which thrives because of social inequality?" [1]

Stonewall later faced a backlash from a large coalition of gay and civil rights groups, including OutRage!, which collectively formed the Coalition for Marriage Equality and argued that the new Civil Partnership Bill created a separate yet equal system "not unlike apartheid". Many LGBT individuals unconnected with these groups took a different view and Stonewall saw a surge in the number of its individual supporters in the wake of the introduction of civil partnership. Between them, almost 10,000 individual donors now contribute significantly more to Stonewall than its income from corporate sources.

One of Stonewall's fiercest critics is Daily Mail columnist, Richard Littlejohn. It is his assertion that Stonewall has become "a byword for intolerance, bigotry and bullying", and often refers to prominent members as "professional homosexuals".